It appears that Apple added a polarity-sensitive sensor to the new iPad, and that the original Smart Covers were made with magnets facing in either direction. Later model Smart Covers don't exhibit this behavior. We can only assume Apple made an adjustment when it refreshed the line in October.

Mark had help from an independent case manufacturer in sussing out the problem. You'll find all of the details here. He also pointed out that if you have an incompatible Smart Cover you can get it swapped out at the Apple Store.